Colitis cystica profunda (CCP) is a rare, benign disease of colorectum. To the naked eye, it is a cystic mass of the colorectum with ulceration on the surface. Pathologically, the cyst is filled with mucus and can grow down into the submucosa, lamina propria, and even serosa. The inner wall of the cyst is covered with mucosal epithelial cells and there is no evidence of malignancy. The focus of this disease is to differentiate it from mucinous adenocarcinoma because misdiagnosis can lead to excessive treatment. We reported a case of CCP with partial low-grade intraepithelial neoplasia of the glandular epithelium in a minor patient,and discussed the pathogenesis and prognosis of the disease by reviewing the relevant historical literature.